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VATIS Update Biotechnology . Jul-Aug 2005

VATIS Update Biotechnology is published 4 times a year to keep the readers up to date of most of the relevant and latest technological developments and events in the field of Biotechnology. The Update is tailored to policy-makers, industries and technology transfer intermediaries.

IN THE NEWS

Biotech firms focus on more in-licensing and alliances

A report released by Deloitte Research, a subsidiary of Deloitte Services LP in the United States,has revealed that biotechnology companies are increasingly focusing on in-licensing acquiring the commercial rights to products. Almost 20 per cent of small biotech companies surveyed plan to predominantly in-license with opportunistic selling of the commercial rights to products or outlicensing. Only a little more than one-third of the firms plan to continue on the traditional path of predominantly out-licensing to larger firms.

The study, Critical Factors for Alliance Formation,also found that more than 70 per cent of small biotech companies plan to increase the number of alliances they form over the next three years.The number of big pharma-biotech alliances has increased from 69 in 1993 to 502 in 2004, and the number of biotech-biotech alliances recently exceeded the number of pharma-biotech alliances.

The study found that new biotech companies were becoming formidable competitors for attractive products, and the emergence of specialty pharmaceutical companies that in-license smaller products was also driving competition. As a result, in North America, small biotech companies are choosing from an average of eight candidates for each alliance deal, and the competitive landscape haspushed these alliances to earlier stages of product development.

According to Mr. Matthew K. Hudes,Deloittes National Managing Principal for biotechnology, in order to become alliance partners companies have to focus on commitment from senior management, favourable deal terms, market depth particularly in therapeutics area and firm alignment with the partners core strategy. Mr. GlennSnyder, a Principal at Deloitte, says that the most successful companies would be the ones that create a flexible yet efficient approach to building alliance portfolios. The approach which includes strategic planning, identifying and accessing potential partners, and developing differentiated but mutually beneficial alliances would enable these companies to drive sustained growth in the future.

Chemical Weekly, 12 July 2005

EU ministers uphold right to ban GMOs

European Union environment ministers dealt a blow in June to efforts to get more GMO crops grown in Europe, as they agreed to uphold eight national bans on genetically modified maize and rapeseed types. The vote was a setback for the European Unions Executive Commission, which had wanted the ministers to endorse an order to lift the bans within 20 days. European Union law provides for national GMO bans if the government can justify the prohibition.

The decision has given an opening to the United States, Canada and Argentina, whose suit against the European Union at the World Trade Organization (WTO) alleges that European Unions biotech policy harms trade and is not founded on science. WTO is expected to issue its initial ruling on the GMO case in early October, officials say.

The ministerial decision was the European Unions first agreement on GMO policy since 1998, when the bloc began its unofficial moratorium on approving new GMO foods and crops, lifted last year by a legal default. Between 1997 and 2000, Austria, France, Germany, Greece and Luxembourg banned specific GMOs on their territory, focusing on three maize and two rapeseed types approved shortly before the start of the moratorium.

The European Unions Executive Commission now has several options, including returning to the ministers with the same proposals for lifting the bans, though at a later date, or changing them radically.

Indian AIDS vaccine trial to focus on immunogenic capacity

The Phase I trial of the Modified Vaccina Ankaara (MVA) or TBC-M4 AIDS vaccine trial on human beings, which is going to commence in October 2005, would focus on assessing the safety and immunogenic capacity of the vaccine. Tuberculosis Research Centre(TRC), Chennai, India would conduct trial. A team of 18 members working in TRC would work with 32 volunteers participating in the trial by using the immunology laboratory in the Centre. The results of this trial would orient further clinical studies to be conducted. The trial of vaccine on human beings may take approxi-mately two years. This is the second AIDS vaccine to be tried on humans in India. The Ministry of Environment and Forests Genetic Engineering Approval Committee (GEAC) had given approval for the trial on 8 June2005. ICMR initiated human trial of the Adeno Associated Vector Borne Vaccine (AAV) in the beginning of 2005. The vaccine, manufactured by Theroin Biologica Corporation of the United States, was first vaccine that ICMR tried on human being.

Chronicle Pharmabiz, 23 June 2005

Indian state to set up biotech park

The state of Himachal Pradesh, India, is setting up with private sector partnership a US$44.4 million biotech park at Kotla-Barog near Solan. About 140 acres by the side of Solan-Rajgarh highway have been identified for the purpose. The biotech park will have an incubation facility of international standards and a state-of-the art biotechnology industry cluster to be set up under the publicprivate partnership model.

The first phase of the project would involve setting up the incubation facility in an area of 25 acres. The facility would have an investment of about US$8.1 million of which US$3.67 million would be from the government. Of the US$3.67 million, US$2 million would come from the central government and the state government would contribute the remaining. The incubation facility would offer various services including lab space for start-up companies, educational programmes and assistance in product commercialization, R&D and technology transfer, a well-equipped production facility, and value addition and extraction units for business enterprises and farmers. The private partner is to be chosen soon and the required equipment for the incubation facility obtained by the end of July 2005. The incubator is expected to be ready by early 2006. A Bio-business Society set up by the government will be the nodal agency for managing the biotech park. The states Department of Biotechnology will give technical guidance.

The government is offering special incentives to companies such as central excise duty exemptions for 10 years, income tax holiday for 5 years, sales tax exemption on biotechnology products and special incentive package for mega biotech units with investment more than US$11.1. The biotech park is expected to attract investments from companies in the areas of DNA-recombinant drugs, vaccines, proteins, diagnostic kits for human and animal healthcare, and medicinal plants.

Chronicle Pharmabiz, 13 June 2005

Germany to fund research on green gene technology safety

The German government is to support research into the safety of genetically modified (GM) plants with 10 million over the next three years. Some 24 projects would receive the funding, all of which would investigate the effects that GM plants have on the effectiveness of antibiotics and herbicides.

Seven of the projects would address the replacement of antibiotics and herbicide resistance genes. Antibiotic resistance markers are important tools for the development of genetically modified crops. They are used to identify and isolate the gene or genes that have been moved from one plant to a plant that was to be genetically modified. The researchers would seek to develop methods to remove the marker gene after the creation of transgenic plants, or to ensure that it is only present in a specified area of the genome, in order to avoid unwanted side effects. Nine projects would focus on transgenic varieties of maize, which contains the Bacillus thuringiensis (Bt) gene, resistant to certain insects that damage the root of the crop. The projects would investigate the ecological impact of growing the crops containing Bt, as well as the potential ability of the insects to develop a resistance to the gene. Other projects would look into the biological safety of transgenic cereal crops with resistance to fungus, and the impact of growing transgenic potatoes on the quality of the land.

MARKET NEWS

New study finds overcapacity in biopharma industry

A second market research report has found the market capacity for contract manufacturing of biopharmaceuticals to be in excess, in contrast to the hitherto prevailing wisdom that the sector has been suffering from undercapacity. The report,published by HighTech Business Decisions, suggests that in 2004 and 2005, the industry has a slight excess of capacity, as new capacity continues to come online in and process improvements are being made. This ties in with recently published research from Frost & Sullivan, which predicted that biomanufacturing will be in overcapacity through to 2011.

The biopharmaceutical contract manufacturing industry is undergoing significant changes as it matures to a stable and reliable resource for the manufacture of biologics, according to HighTech. In addition to new expression technologies, cell line development, and biomanufacturing platforms offered for mammalian cell culture and microbial fermentation, some contractors are gearing up to produce novel product types that require specific biomanufacturing expertise such as antibody fragments, fusion proteins, antibody drug conjugates, gene therapy and novel proteins. The market for biopharmaceutical contract manufacturing reached US$1.7 billion in 2004, with healthy growth forecast for 2006.

Wyeth Biopharma and Dublin City University cooperate for research

Ireland-based Wyeth BioPharma, the biopharmaceutical unit within Wyeth Pharmaceuticals, has entered into a four-year research agreement with Dublin City University (DCU) in Ireland to generate scientific knowledge that would facilitate the creation and industrialization of biopharmaceutical production.

Scientists at Wyeth BioPharmas campuses at Grange Castle in Dublin and at Andover, Massachusetts,the United States, together with their counterparts at the National Institute for Cellular Biology at DCU would use Wyeths proprietary Chinese Hamster Ovary (CHO) cell technology and gene expression profiling to examine cell performance under industrial production conditions.In this partnership, DCU, with support of 4 million from Science Foundation of Ireland (SFI), would provide research personnel and expertise, proteomics and full-length gene cloning technology. Wyeth would make a comparable commitment in the form of research personnel and expertise, proprietary CHO cell lines, cell culture process and CHO chip technologies, and gene sequencing. Both groups would contribute to the mRNA expression profiling, bioinformatics and functional evaluation aspects of the joint research programme.

Attaining the ability to produce these therapeutic proteins in sufficient quantities is the greatest challenge that the biopharmaceutical industry faces, according to Dr. Maurice Treacy, SFIs Director of Biotechnology. An estimate indicates that the industry must increase cell culture capacity by five or six times to meet future demands.

Metabasis and Merck team up for new small molecule therapeutics

In the United States, Metabasis Therapeutics Inc.and Merck & Co. Inc. have formed a collaboration to research, develop and commercialize novel small molecule therapeutics with potential to treat several disorders including hyperlipidemia, type II diabetes and obesity by activating an enzyme called AMP-activated protein kinase in the liver.

Both firms would conduct discovery efforts and contribute drug candidates to the collaboration. Merck would make a payment of US$5 million on signature of the agreement and would provide Metabasis with funding for its research contribution to the programmes. It assumes primary responsibility, including financial responsibility, for clinical development of any resulting product candidates and would have the right to market such products worldwide. Metabasis would be eligible to receive payments upon achievement of certain milestones during development of a product candidate.It would receive a royalty on net sale and have the option to co-promote the product in the United States.

Chronicle Pharmabiz, 7 July 2005

Open Biosystems to distribute TRCs shRNA libraries

Open Biosystems Inc. based in California, the United States, has entered into a non-exclusive agreement with the Broad Institute of MIT and Harvard to distribute The RNAi Consortium (TRC) lentiviral shRNA libraries. The Expression Arrest-TRC shRNA libraries extend Open Biosystems portfolio of RNAi resources, providing life science researchers worldwide access to the most extensive vector-based RNAi collections available.

TRC would create the materials needed for RNAi experiments on 15,000 human and mouse genes each. Composed of short hairpin RNA (shRNA) sequences designed to reduce the expression of specific human and mouse genes, it would create and validate these genome-wide libraries. Open Biosystems would manufacture, evaluate and market the shRNA libraries to scientists worldwide.

A powerful feature of this and other viral-based shRNA libraries is that they could be efficiently transformed into viral particles and easily introduced into cell lines routinely used in biomedical research. This includes cancer cells, neurons and other primary cells normally resistant to transfection-based delivery. The librarys 47,500 shRNA constructs of 9,500 human and mouse genes would be on expanded quarterly until all 150,000 constructs are completed.

Roche opens worlds largest PCR facility

Roche Diagnostics, the United States, has opened the worlds largest Polymerase Chain Reaction (PCR) manufacturing site in the world, investing more than US$150 million. The facility, located in Branchburg, New Jersey, is to manufacture and supply Roche Diagnostics PCR technology and produce PCR kits for the research, diagnostic and blood screening markets. The new 26,000 m2 facility would employ up to 800 people, creating approximately 350 new jobs.

The diagnostic kits are used for the detection and quantification of infectious diseases such as HIV, hepatitis and sexually transmitted diseases, as well as for blood screening. The production range of company includes reagents for a variety of diagnostic platforms, including microarray technology used in AmpliChip Tests. Overall, Branchburg produces approximately 140,000 kits per month, which are distributed worldwide. Roches latest expansion reflects its growing presence in the world market.

Dynavax initiates Phase 3 trial for hepatitis B vaccine

Dynavax Technologies Corporation, California,the United States, has announced the initiation of a pivotal Phase 3 clinical trial of its hepatitis B (HBV) vaccine in an older adult population that was difficult to immunize with conventional vaccine.The vaccine has been designed to compare its effectiveness with that of Glaxosmithklines Engerix-B HBV vaccine. A second pivotal Phase 3 trial in a younger adult population in Europe and Canada is anticipated to begin in early 2006.

Dynavaxs HBV is based on its proprietary immunostimulatory sequence (ISS) that specifically targets Toll-Like Receptor 9 (TLR-9) to stimulate an innate immune response. The vaccine combines ISS with HBV surface antigen (HbsAg) and was designed to significantly enhance the level, speed and longevity of protection. The Phase 3 trial would enrol more than 400 seronegative adults aged 40-70, and would take place at study sites in Singapore, Taiwan, Korea and the Philippines. One group would receive three doses of Engerix-B administered at a dose of 20 g HbsAg plus three milligrams of ISS, by intramuscular injection at zero, two and six months. The other group would receive three doses of Engerix-B administered at a dose of 20 g HbsAg through intramuscular injection at zero, one and six months.

Dynavax has previously reported that the primary endpoint analysis of a randomized, double-blind Phase 2/3 trials in older adults showed statistically significant superiority in protective antibody response and robustness of protective effect after three vaccinations compared with Engerix-B. The results of a double-blind Phase 2 clinical trial on young adults (18-28 years) also showed that protective antibody response was achieved faster (two vaccinations over two months compared with three over six months) and were maintained longer with Dynavaxs HBV vaccine than with Engerix-B.

Express Pharma Pulse, 7 July 2005

GENOMICS

Study turns spotlight on junk DNA in higher eukaryotes

A ground-breaking comparative genomics study by a group led by Dr. Adam Siepel at the University of California, Santa Cruz, the United States, has made the most comprehensive comparison to date of conserved DNA sequences in the genomes of vertebrates, insects, worms and yeast.One of their major findings was that as organism complexity increased, so did the proportion of conserved bases in the non-protein-coding (or junk) DNA sequences. This finding clearly underscores the importance of gene regulation in more complex species.

Dr. Siepels team aligned whole-genome sequences for four groups of eukaryotic species (vertebrates, insects, worms and yeast). The vertebrates included human, mouse, rat, chicken and pufferfish, and the insects included three species of fruit fly and one species of mosquito. Two worm species and seven yeast species rounded out the set. To help ease the task, the researchers developed a new computational tool called phastCons. The tool allows for multiple substitutions per site, accounts for unequal substitution rates for different nucleotides, and considers the phylogenetic relationships of the species involved. Using phastCons, the researchers estimated that only between 3-8 per cent of the human genome was conserved in the other vertebrate species. On the other hand, the more compact genomes of insects were more highly conserved (37-53 per cent), as were those of worms (18-37 per cent) and yeast (47-68 per cent).

Most strikingly, two-thirds or more of the conserved DNA sequences in vertebrate and insect species were located outside the exons of protein-coding genes, while non-protein-coding sequences were only about 40 per cent and 15 per cent of the conserved elements in the genomes of worms and yeast, respectively. These new findings tend to support the hypothesis that increased biological complexity in vertebrates and insects derives more from elaborate forms of regulation than from a larger number of protein-coding genes.

Genetic codes of three deadly parasites cracked

A team of scientists led by Dr. Najib El-Sayed of The Institute for Genomic Research (TIGR), the United States, has decoded the entire genetic sequences of parasites that cause three of the deadliest diseases in the developing world leishmaniasis, sleeping sickness and Chagas disease.These neglected diseases kill more than 150,000 people every year. All these have about 6,200 genes in common. Research to identify drug targets would focus on these shared genes. The US$32 million sequencing project involves a major collaborative effort of scientists from TIGR, the Seattle Biomedical Research Institute, the Sanger Institute all based in the United States and the Karolinska Institute in Stockholm.

The parasite that causes sleeping sickness evades our immune systems by creating a smokescreen of millions of molecules on its surface. The team found that many of these were made by combining the products of pseudogenes genes that were no longer fully functional but could still make fragments of proteins. There were so many combinations of these fragments available that the parasite can keep changing the types of molecules appearing on its surface. This allows the parasite to continually evade being detected and destroy by the immune system. The surface molecules were arranged in such a complex way that scientists are unlikely to find a single parasite antibody that could form the basis of a vaccine.

The next step for drug researchers is to discover the function of genes all three parasites share by blocking them and seeing what effect this has on the parasites.

Scientists sequence genome of beneficial bacterium

A team of scientists led by Dr. Joyce Loper, plant pathologist at the United States Agricultural Research Service (ARS) has determined that the bacterium Pseudomonas fluorescens (Pf-5), which is composed of 7.1 million base pairs, naturally safeguards roots and seeds from infection by harmful microbes that cause plant diseases and is expected to greatly benefit crop plants. Two decades ago, scientists found the Pf-5s ability to suppress two major cotton diseases. Since then, plant pathologists around the world have used this strain as a laboratory model to investigate beneficial microbes. The use of naturally occurring, beneficial microbes such as Pf-5 to control plant pathogens is also gaining momentum as a preferable way to grow healthy plants without using synthetic fungicides.

Dr. Loper predicts that the new genomic data would help scientists to more quickly develop new ways to boost the effectiveness of beneficial microbes in fighting plant diseases. This genomic sequence has revealed previously unknown traits of Pf-5 that increase its potential for biological control. This project also pioneered a new methodology that relies on analysis of repeated regions of the DNA sequence to help identify segments of the genome that appear to have been transferred from other microbes.

Genetic on-off switches pinpointed in human genome

Researchers led by Dr. Bing Ren and Dr. Tae Hoon Kim at University of California, San Diego, the United States, have discovered the location and sequence of over 10,000 DNA regions that function as genetic on-off switches or promoters in human fibroblasts. Fibroblasts are relatively generic, easily maintained human cells that form connective tissues throughout the body. By knowing the specific sequences of DNA that control the nearly 8,000 active genes in fibroblasts, scientists can tease apart the biochemical regulation system these cells use to turn genes on and off during normal growth.

To accomplish the genome-wide promoter survey,the researchers designed a novel experimental procedure based on cutting-edge microarray technology. They reported that multiple promoters often control a single gene in parallel, adding another layer to an already complex genetic regulation mechanism. They also discovered promoters in front of DNA sequences not previously recognized as genes. The promoter map would not only provide new insight into how genes were controlled in fibroblasts, but also serve as a framework for the analysis of genetic control in other human cell types, tissues and perhaps organs.

Understanding the on-off control mechanisms would further the knowledge on how a cell is programmed to perform certain specialized functions.

Hundreds of novel human microRNAs identified

Scientists led by Dr. Isaac Bentwich, founder and chairman of Rosetta Genomics in Israel, have reported the identification of hundreds of human microRNA genes, including primate-specific micro-RNAs. They successfully cloned and sequenced 89 human microRNAs, nearly doubling the number sequenced in humans to date.

MicroRNAs are a recently discovered class of tiny regulatory genes, comprised in the 98 per cent of the genome that does not encode proteins, which until recently were considered Junk DNA. Micro-RNA genes are of central importance, regulating at least 30 per cent of all proteins, and involved in a wide range of diseases, including diabetes, obesity, viral diseases and various types of cancer. Primate-specific microRNAs support the notion that these play an important role in the evolution of complexity of higher organisms. These genes may serve as an important basis for next generation diagnostics and therapeutics.

Jumping genes in the brain

Dr. Fred Gage and his team at the Salk Institute for Biological Studies, California, the United States,have reported that genetic elements that jump around the genome could influence brain circuitry. In a study of rat adult hippocampus neural stem cells, they discovered an up to two-fold enrichment of the transcripts of retrotransposons known as L1 elements, which jump around the genome and comprise roughly 20 per cent of mammalian genomes.

The researchers used a human L1 engineered with an enhanced green fluorescent protein that activated only when the entire construct underwent retransposition. In mice bearing this construct, immunofluorescence microscopy revealed fluorescence only in germ cells and brain tissue. Moreover, fluorescence was only seen in neurons and not in astrocytes or oligodendrocytes. Looking for regulators of L1 activity, the researchers foundthat human L1 contained two binding sites for Sox proteins, which were expressed in brain and testis. RNA interference showed that a 75 per cent decrease in Sox2 in neural stem cells led to a six-fold increase in L1 expression. They also showed that the decrease in Sox2 activity coincided with changes in genomic acetylation and methylation, suggesting L1 activity was regulated by accessibility to open areas of DNA. Dr. Gage and colleagues then used inverse PCR to reveal that L1s can insert within neuronally expressed genes. Rat adult hippocampus neural stem cells harbouring detectable retranspositions tended to differentiate into neurons rather than glial cells, revealing L1s can affect cell fate.

Gene for Immune Deficiency Syndromes found

A team of researchers led by Dr. Raif Geha and Dr. Emanuela Castigli, from the Division of Immunology at Childrens Hospital Boston, the United States, has discovered that gene mutation may account for many cases of immune deficiency, in particular the two syndromes known as Immunoglobulin A (IgA) Deficiency and Common Variable Immunodeficiency (CVID). IgA deficiency affects 1 in 600 people, while CVID is less common but more severe. Children and adults with either condition suffer relentlessly recurring ear, sinus and gastrointestinal infections, as well as bronchitis and pneumonia. IgA deficiency and CVID could occur in the same family, and predispose people to autoimmunity, particularly affecting the thyroid gland and resulting in thyroid hormone insufficiency.

The researchers found mutations in a gene known as TACI in 4 of 19 unrelated patients with CVID and in 1 of 16 unrelated patients with IgA deficiency. None of 50 healthy people tested had a TACI mutation. Further study of 4 of the 5 patients with TACI mutations revealed that all had relatives with the same mutations. Eleven of the 12 identified relatives with TACI or IgA deficiency had a history of recurrent infections, and low levels of immunoglobulin A (IgA), immunoglobulin G (IgG) or both. TACI mutations interfere with two aspects of the immune response that involve maturation of B cells, the white blood cells that make immunoglobulins, which function as antibodies to fight infections. Normally, TACI triggers B cells to switch from making immunoglobulin M (IgM), an antibody produced early in the bodys immune response, to making other immunoglobulins like IgA and IgG. More important, TACI signals B cells to produce antibodies with a high affinity for specific attackers. Because TACI mutations are dominant, people with even one copy of the mutation would be unable to mount a strong antibody response.

Biochemical switch that regulates cell division

Scientists at St. Jude Childrens Research Hospital,the United States, and Technical University of Munich, Germany, have found that cells control mitosis by assembling a biochemical switch to block it or by disassembling the switch to trigger it. When the switch called SCF-NIPA is intact, levels of the enzyme Cyclin B1 drop, preventing the enzyme from activating a third protein called Cdk1. By blocking the interaction between Cyclin B1 and Cdk1, SCF-NIPA prevents the cell from dividing.

This study explains how cells delay the onset of mitosis until the DNA in the nucleus has been properly duplicated and prepared for transport into the daughter cells that would arise when the cell divides, and how SCF-NIPA is also the key that controls the level of that protein.

Researchers found that Nuclear Interaction Partner of ALK, or NIPA, is the timing device that determines when SCF-NIPA triggers mitosis. When phosphate molecule is attached to NIPA, it cannot bind to Skp-Cullin-F box (SCF). The level of Cyclin B1 rises during this time, which occurs when the cell is completing the duplication of its DNA (S phase), as well as during the subsequent preparatory phase (G2 phase) and the early part of mitosis (M phase).

When it sheds the attached phosphate molecule, NIPA binds to SCF to form SCF-NIPA. The addition of NIPA makes SCF specifically target Cyclin B1, sending that molecule to the proteasome, the cells protein-degradation machine. This degradation of Cyclin B1 occurs during the cells resting phase, or interphase. In the absence of Cyclin B1 during interphase, the protein Cdk1 cannot trigger mitosis. While this process was known, the current study explains how it is regulated. It also showed that blocking the production of NIPA in a cell causes the cell to start dividing prematurely.

MEDICAL BIOTECH

Scientists create way to generate brain cells in lab

A team of scientists led by Dr. Bjorn Scheffler, at the University of Florida College of Medicine, the United States, has created a system in rodent models that for the first time duplicates neurogenesis the process of generating new brain cells in a dish. If the discovery could translate to human application, it would enhance efforts aimed at finding ways to use large number of a persons own cell to restore damage brain function, partially because the technique produces cells in far greater amounts than the body could generate on its own.

According to Dr. Bjorn Scheffler, a neuroscientist with the College of Medicine, It is like an assembly line to manufacture and increase the number of brain cells. We can basically take these cells and freeze them until we need them. Then we thaw them, begin a cell-generating process, and produce a tonne of new neurons. The researchers have isolated for the first time what appears to be the true candidate stem cell. Their work holds the potential to heal disorders such as Parkinsons disease or epilepsy.

Chronicle Pharmabiz, 23 June 2005

Study shows adult stem cells ability to self-renew

Dr. Johnny Huard and his team at the Growth and Development Laboratory, Childrens Hospital of Pittsburgh, the United States, have discovered that adult, or post-natal, stem cells have the same ability as embryonic stem cells to multiply. This is a previously unknown characteristic indicating that post-natal stem cells may play an important therapeutic role. The researchers were able to expand post-natal stem cells to a population level comparable to that reached using embryonic stem cells. It has been believed that embryonic stem cells have a greater capacity to multiply than post-natal stem cells, making them more desirable to research as a potential treatment. Previous research had found that embryonic stem cells could undergo more than 200 population doublings before they began to die.

Dr. Huards team discovered that a unique population of muscle-derived stem cells was able to undergo more than 200 population doublings as well. These post-natal cells were able to undergo population doublings while maintaining their ability to regenerate muscle in an animal model, a key finding indicating that they could maintain their treatment potential. This ability to self-replenish is significant because in order for stem cells to be used for treatment, a large quantity of the cells would be required. Furthermore, post-natal stem cells have advantages in autoimmunity. Issues of rejection could complicate the use of embryonic stem cells, with the recipients immune system rejecting the foreign embryonic stem cells. This would be avoided with post-natal stem cells taken from the recipient and reintroduced in an autologous manner.

Trial of ABthrax in anthrax prevention and treatment

Dr. Mani Subramanian and colleagues at Human Genome Sciences Inc., Maryland, the United States,have validated the safety and efficacy of ABthrax, the first investigational agent against anthrax infection to be evaluated in a clinical study since the 2001 anthrax attacks in the United States. The trial results proved that the agent was safe and well tolerated, and achieved the blood levels necessary to afford significant protection from the lethal effects of the anthrax toxin.

Anthrax infection is caused by Bacillus anthracis, which multiplies in the body and produces lethal toxins. Research has shown that protective antigen to be the key facilitator in the progression of anthrax infection at the cellular level. After protective antigen and toxins are produced by the bacteria, protective antigen binds to the toxin receptor on cell surfaces, forming a protein-receptor complex that facilitates the toxins entry into the cells.

ABthrax, a fully human monoclonal antibody to Bacillus anthracis protective antigen, was studied in a randomized, single-blind, placebo-controlled, dose-escalation Phase 1 clinical trial in 105 healthy adult volunteers. The trial was designed to evaluate the safety, pharmacokinetics and biological activity of ABthrax. Two separate intramuscular injection sites were evaluated. Pharmacokinetics, immunogenicity and parameters of biological activity werealso evaluated. Results showed ABthraxs safety, tolerance and bioavailability after a single intramuscular or intravenous dose, with no dose-limiting adverse events. Only transient, mild-to-moderate adverse events were observed, with no statistically significant difference in adverse event profiles between active and placebo arms of the study. Unlike the anthrax vaccine, the protection afforded by a single dose of ABthrax would be immediate following the rapid achievement of appropriate blood levels of the antibody. In contrast to antibiotics, ABthrax acts against the lethal toxins produced by anthrax bacteria. It may also prevent and treat infections by antibiotic-resistant strains of anthrax.

Scientists uncover key Parkinsons clue

Researchers at the University of Texas Southwestern Medical Centre, Dallas, the United States,have identified a mechanism that causes proteins to clump together in the brain cells of Parkinsons disease patients. As the proteins clump together, they inhibit an enzyme that normally breaks them down, leading to even more protein clusters.

The study led by Dr. Philip Thomas identified a specific protein, alpha-synuclein, as the culprit. Normally, when a cell is stressed, alpha-synuclein unfolds and an enzyme degrades the protein into harmless pieces that cannot clump together. But in people with Parkinsons disease, there is a malfunction in some of the degrading enzyme, leaving shortened sections of unfolded alpha-synuclein instead of the more harmless pieces. These intact sections of alpha-synuclein act like seeds, collecting other unfolded sections of the protein around them. It takes only a few molecules of such fragments to start the Parkinsons process.

Stem cell finding offers IVF hope

At the Centre for Stem Cell Biology in Sheffield, United Kingdom, scientists have shown that embryonic stem cells could develop into the earliest stages of eggs and sperm. In principle, it may be possible to clone stem cells from an infertile patient and turn these into the required sperm or eggs for in vitro fertilization (IVF). The team used stem cells from embryos donated for research by couples undergoing IVF and found some formed into a collection of cells called embryoid bodies. When they looked at these cells in detail they found that within two weeks a small number of cells expressing some of the genes found in human primordial germ cells were present. Some cells also expressed proteins only found in maturing sperm.

According to Dr. Behrouz Alfatoonian, a member of the research team, the challenge now was to choose the cells that were going to develop into primordial germ cells and then work out how to encourage them to grow into mature sperm and egg. Producing functional gametes is more difficult because the scientists will have to recreate for the cultured cells the environment of the developing follicle for the egg or the tissue of the testis for the sperm.

Harmless virus kills some cancers

In the United States, scientists led by Dr. Craig Meyers, at the Penn State College of Medicine, and the Penn State Milton S. Hershey Medical Centre have reported that Adeno-associated virus type 2 (AAV2), which infects the majority of the population but has no known ill effects, kills many types of cancer cells yet has no effect on healthy cells. This suggests that AAV2 has great potential to be developed as an anti-cancer agent.

Population-based studies have shown that people who carry AAV2 tend not to develop human papillomavirus (HPV) associated cervical cancer. In general, AAV2 requires association with a helper virus in order to replicate. When it finds a helper virus, such as HPV, AAV2 disrupts the life cycle of the host and induces apoptosis or cell death. Even without co-mingling with another virus, AAV2 seems to be able to infect and express itself in other types of cancer cells also disrupting their ability to survive and inducing cell death.

Dr. Meyers team first used HPV infected epithelial cells and normal human epithelial cells, which are natural hosts for both AAV2 and HPV. In cultures infected with both AAV2 and HPV, they found that after six days, all HPV infected cells had died. The same approach was used in four types of cancer cervical, breast, prostate and squamous cell, all epithelial cell cancers all cancer cellswere dead in six days. Though previous studies have investigated the cancer-targeting potential of AAV2, none allowed the AAV2 to remain in culture long enough to see the effect now uncovered. According to Dr. Meyers, one of the most compelling findings is that AAV2 appears to not have any pathologic effects on healthy cells. So many cancer therapies are as poisonous to healthy cells as they are to cancer cells. A therapy that is able to distinguish between healthy and cancer cells could be less difficult to endure for those with cancer. Future studies would investigate the mechanisms through which AAV2 causes cancer cell death, and how the virus might be made to more actively target and kill cancer cells.

Cell transplants may protect brain tissues in MS-like disease

A team of researchers led by Dr. Stefano Pluchin at San Raffaele Hospital, Milan, Italy, has reported that immature nerve cells (adult mouse neural stem cells) injected into the blood of mice with disease like multiple sclerosis (MS) were able to suppress the immune attacks that damage the brain and spinal cord tissues. This suggests that neural stem cells in the adult brain may not only serve as replacement cells for tissue repair but, in some circumstances, also protect the brain from inflammation.

Research has shown that adult brains contain stem cells that might serve as replacement cells. Transplantation of immature myelin-making cells has been to some degrees successful in rodents. However, such repair has only been successful in isolated areas of the brain, whereas MS and MS-like diseases in animal models involve lesions scattered throughout the brain and spinal cord. Finding a way to introduce replacement cells that could migrate throughout the central nervous system and home in on damaged areas has been a significant hurdle. The current study attempted to define the mechanisms responsible for the migration of these cells into the brain and to sites of injury.

They injected neural stem cells, taken from the brains of adult mice, into the blood of mice with a relapsing-remitting form of EAE, an MS-like disease. Some mice were injected at the onset of disease and others at the onset of the first relapse. Mice in which neural stem cells were injected at disease onset started to recover in 30-60 days, and experienced a two-fold reduction in relapses compared with untreated mice. Mice injected at the first relapse started to recover later, but showed a three-fold reduction of the relapse rate in 60- 90 days, compared with untreated mice. Both groups showed a significant reduction in the extent of myelin damage and nerve fibre loss compared with untreated mice.

The team then explored the mechanism by which the neural stem cells entered the brain from the bloodstream. They reported that a protein on the cell surface called VLA-4 facilitated cell movement into the brain. In addition, the team reported finding a wide range of immune proteins to be active on the transplanted neural stem cells; these proteins serve as docking sites to receive signals from immune cells active in the attack. Furthermore, a portion of the transplanted cells remain in an immature state and accumulate in the brain around blood vessels (perivascular areas) where immune cells enter the brain during active disease. These transplanted cells show signs of being able to turn off activated immune cells and reduce inflammation, thus protecting brain tissues from immunemediated damage.

Stem cell guide may be key for neural stem cell treatments

Dr. Qun-Yong Zhou and Mr. Kwan L. Ng at the University of California Irvine School of Medicine,the United States, have discovered how new neurons born from endogenous neural stem cells are sent to regions of the brain where they could replace old and dying cells. They have identified a protein, a small peptide called prokineticin 2 (PK2), that play a key regulatory role for the proper functional integration of these new neurons in the brain. PK2 guides the migration of neurons born from neural stem cells from the subventricular zone in the brains core through mature tissue to reach the olfactory bulb, the smell part of the brain located above the sinus cavity. PK2 allows these new neurons to settle into the proper areas of the olfactory bulb to function normally. According to Dr. Zhou, PK2 is an attractive drug target for boosting neuronforming processes or stem cell-based therapies for diseases like Alzheimers and Parkinsons, or for stroke and other brain injuries.

Express Pharma Pulse, 7 July 2005)

PROTEOMICS

Master switch in cell death discovered

A team of researchers led by Dr. Qing Zhong at the University of Texas Southwestern Medical Centre, the United States, has found an enzyme vital for controlling the early stages of cell death a beneficial and normal process when it works right, but malignant in a variety of cancers when it goes wrong. The life and death of cells is a complex avalanche of reactions, controlled by a few molecules that sit atop a biochemical pyramid. The newly discovered enzyme, named Mule, destroys a key molecule at the top of the pyramid, thus leading to the cascading disintegration of the cell. These findings also suggest a new drug target for controlling tumor formation.

Researchers found the interaction between the Mule enzyme and a major player in cell death, the protein Mcl-1. While there are many possible routes a cell may take towards apoptosis, this interaction serves as one of the master switches controlling which of those pathways are triggered. Normally, Mcl-1 keeps cells alive by protecting them against apoptosis. A healthy organism needs just the right amount of Mcl-1 too little of it could lead to a damaged immune system or even death; too much of it would keep cells alive abnormally, leading to cancers such as lymphomas. Using human cell extracts, the researchers found that Mule caused the protein ubiquitin to bind to several sites on Mcl-1, serving as a flag for that molecule to be destroyed. The interaction between Mule and Mcl- 1 might be manipulated to help cancer patients, with the treatment focusing on the biochemistry of Mule and Mcl-1.

Enzymes newly discovered role may help target arthritis

A team of scientists led by Dr. Christine Pham, at Washington University School of Medicine, Washington, the United States, has found a new role for a previously identified enzyme, CathepsinG, that may make it a target for anti-inflammatory treatments. CathepsinG regulates the ability of immune cells known as neutrophils to secrete chemicals that attract other immune cells and start the local inflammatory process. Over time, the excessive accumulation of immune cells can lead to tissue and cartilage damage in joints, causing pain and limiting mobility. CathepsinG, which is made by the neutrophils it regulates, is also an attractive target because it belongs to the class of protease enzymes: one principal HIV treatment inhibits proteases.

Dr. Phams team injected mice with collagen from calf joints. The mice make antibodies to that protein. The antibodies have enough cross-reactivity that they would bind to the mouses own cartilage and collagen and initiate an inflammation. This leads to a condition similar to rheumatoid arthritis in the mice. Observations made by Dr. Phams team and others had linked the earliest stages of inflammation in the animal models to neutrophils, which arrive first at sites of injury, infection or irritation and secrete chemicals that bring in secondary waves of other immune attack cells.

Dr. Phams team showed that CathepsinG was secreted by neutrophils, binds to the cells surface membranes and affects the rearrangement of integrins, an important group of adhesion compounds on the surface of neutrophils. The way integrins rearrange and cluster on the cell surface could send a signal back into the cell that modifies the cells behaviour, allowing it to do things like secrete inflammatory factors. The ability of proteases to affect integrin rearrangement depends on their catalytic activity and that can be taken away from them.

A protein in the eye may prevent eye diseases

At The Schepens Eye Research Institute in the United States, scientists led by Dr. Joan Stein- Sreilein have discovered that a protein known as F4/80 found on immune cells of the body may have a function in the regulation of the bodys immune response and protection of delicate tissues that cannot survive the inflammation inherent in fullblown immunity.

Certain parts of the body including the eyes, brain, gastrointestinal system and reproductive system have the ability to prevent the usual immune response onset when confronted with foreign invaders such as bacteria. Without this reaction, the eyes delicate tissue would be destroyed by inflammation and the gastrointestinal tract cannot tolerate the ingestion of food. The glycoprotein F4/80 was discovered two decades ago, but its function has not been understood. In previous studies, the team found that when F4/80- containing cells bring antigens from the eye to the spleen, the spleen stimulates the production of regulatory T cells that stop the immune response throughout the body as well as at the site where the invasion took place (the eye). In a fullblown immune response, other types of T cells are stimulated to start the immune attack, inflammation and tissue destruction.

The team investigated mice that did not produce F4/80 and found that the immune suppression did not occur when foreign substances were introduced to the spleen by antigen-presenting cells that did not have F4/80, showing the proteins direct role in immune suppression. The exclusion of the protein from T cell zones in the spleen suggests that F4/80 expression and immune activation may be mutually exclusive. These findings may lead to novel therapies for autoimmune diseases of the eye and the body.

Researchers show protein routes messages in nerve cells

Nerve cells relay messages at blink-of-the-eye speeds by squirting chemicals called neurotransmitters across tiny gaps called synapses to awaiting message receptors. But different receptors and neurotransmitters work simultaneously which goes where to send the proper message? A team of researchers led by Dr. David Featherstone at University of Illinois, Chicago, the United States, studied this issue using the common fruit fly as their research animal and the chemical glutamate present in fruit flies and humans as the neurotransmitter of choice.

The team found that the protein coracle known as 4.1 in humans links receptors on a nerve cells membrane to its internal structure, or cytoskeleton. Since 4.1 only interacts with certain receptor proteins, it functions as a sorting agent to ensure that the correct type of receptor gets attached. The researchers also identified the cytoskeleton proteins called Actins to which the receptors tie. It is still unknown how glutamate receptors get to precisely where they were supposed to go on a cell in order to mediate the neurotransmission. If the receptors are not the right type or in the right place, then the message gets mixed up or becomes less efficient. Such mix-ups could lead to synaesthesia, where, for example, a sound may have taste, or an image may have a smell. Confirmation of the mechanisms in a mammal could help researchers understand how nerves need to be reconnected after spinal cord injury, or may open doors to developing drugs that could manipulate proteins that cause neurological diseases in humans.

Novel enzyme exhibits promiscuous catalytic activity

Scientists at Salk Institute for Biological Studies, California, the United States, have isolated and studied a new enzyme that could mix and match biochemicals to create a wide range of different molecules that could be used as the basis for new drugs. The enzyme, named Orf2, takes chemical building blocks know as small aromatic molecules and alters them by adding a fat-like molecule called a prenyl group. This alteration could have a huge impact on where the aromatic molecule goes within the cell, and what sort of effects it has when it reaches its target. The researchers tested whether the new enzyme could modify a wide range of small aromatic molecules, ranging from plant flavonoids to olivetol, a component in the production of THC, the activity ingredient of marijuana. They found that Orf2 was able to attach prenyl groups to most of the different aromatic compounds tested. The key to Orf2s flexibility seems to reside in the active site.In many enzymes, the structure of the active site only allows one specific molecule to interact with it, like a key fitting into a lock. But Ofr2s active site was a surprisingly spacious barrel-like structure, unlike any protein fold ever seen before. Not only does this wide barrel allow Orf2 to act on a wide range of aromatic molecules, its discovery could also help expalin the relationship between an enzymes structure, the way it has evolved, and the chemical reactions it is able to carry out. Orf2 could be powerful tool for creating biologically active compounds that could be used as drugs.

Chemical Weekly, 5 July 2005

AGRI BIOTECH

Gene involved in cell suicide mechanism identified

A team of researchers led by Dr. Savithramma Dinesh-Kumar, at the Yale University, Connecticut, the United States, has identified a gene that regulates the major immune response in plants, programmed cell death (PCD). To protect themselves from viruses, plants create a zone of dead cells around an infection site, thus preventing the infection from spreading. The researchers have discovered how the plants keep from killing themselves after they turn on the PCD process.

The team identified and silenced a pro-survival gene, BECLIN-1, that is important in the PCD response. When BECLIN-1 is active, infection is localized to a small number of cells, which later die and form discrete brown lesions on the leaves. When the gene is inactivated, the plant cannot regulate PCD, leading to cell death throughout the leaf and plant. This work gives a better understanding of how plants fend off microbial attacks through carefully controlled destruction of infected cells and throws light on similar processes that occur in mammals, and may eventually be used to better human health.

Plant vaccine targets SARS

Researchers led by Dr. Hilary Koprowski, Director,Centre for Neurovirology, Thomas Jefferson University, the United States, have discovered that tomato and tobacco plants could be engineered to make a vaccine against the SARS virus. To test plants ability to produce a successful SARS vaccine, Dr. Koprowskis team engineered tomato and low-nicotine tobacco plants to produce a fragment of the SARS-CoV protein. Several of the engineered plants successfully expressed high levels of the protein. These levels could be increased through selective plant breeding. To see if the vaccine was effective, the researchers fed mice tomatoes that contained the protein. The mice developed antibodies for the SARS virus. Mice were also treated with a tobaccoderived protein, using injection or via a feeding tube. The injected mice produced SARS-CoV antibodies. However, direct delivery of the protein to the stomach did not produce antibodies. Dr. Koprowskis team speculates that swallowing the tobacco vaccine directly to the stomach does not provide enough exposure to produce antibodies.

Key to rice blast fungus

At Purdue University, Indiana, the United States,a team of researchers led by Dr. Jin-Rong Xu has discovered the molecular machinery that enables blast fungus to find its way into rice plants. The rice blast fungus, Magnaporthe grisea, is the most deadly of the pathogens that attack rice, reducing yields by as much as 75 per cent in infected areas. The team found that an enzyme, called a pathogenicity mitogen-activated protein (MAP) kinase, was a key player in coordinating the fungal attack. The enzyme flips the switch that starts the cellular communication necessary to launch the fungal invasion.

The fungus spreads when its spores are blown to rice plants and stick on the leaves. Once on the plant, the spore forms an appressorium, a bubblelike structure that grows until it has so much pressure inside that it blasts through the plants surface. The researchers found that a pathway, which includes three genes that form a cascade of communication events, drives the infection process. But when genes are blocked, the fungus cannot develop appressoria and infect the plant. The pathway holds enormous potential of being used to produce new fungicides or new resistant rice plants to hold this pathogen at bay.

However, rice blast fungus is able to quickly evolve new tricks to tackle any defence that the rice plants may put up. Researchers also know from sequencing the rice blast genome, that the fungus has a unique family of proteins the G-proteincoupled receptors (GPCR) that act as feelers to tell the fungus when it has a good host plant and how the plant might fight its invasion. Rice blast fungus has more than 40 GPCRs that probably regulate the signals at the beginning of the penetration pathway. The team is now studying the genetic mechanisms that regulate the infection process, how the fungus spores recognize the plant surface and how they know to penetrate it.

Genetic clue to drought-resistant crops

Dr. Josette Masle and colleagues at the Australian National University have isolated a gene that helps Arabidopsis minimize water loss as it grows. This could help scientists grow drought-resistant crops. Plants use pores on their leaves to take in carbon dioxide but lose water through them in the process. The gene, called erecta, determines how many pores the plant has on its leaves and how efficient the cells beneath the pores are at converting carbon dioxide into sugars that the plants use for growth. Erecta is the first gene shown to affect both processes.

Dr. Masles team found that by changing the structure of erecta would create plants with a different balance in the trade-off between losing water and gaining carbon dioxide. Crops, such as rice and wheat, could be helped to be more economical with their water by giving them a version of erecta that strikes the right balance for the environment they grow in. The team has found genetic sequences similar to erecta in rice and wheat, and the crops could be modified through conventional breeding or modern genetic engineering. The research offers the potential to increase yields both in areas already cultivated and on land previously too dry to farm.

Doubly engineered crops better

A team of scientists led by Dr. Anthony Shelton, Cornell University, the United States, has found that insects quickly develop resistance to genetically engineered crops when single-gene plants are grown near double-gened ones. The scientists looked at the history of diamondback moths kept in a greenhouse with genetically engineered broccoli. They found that when moths were kept with plants engineered to produce two types of toxin, all the insects died within 26 generations or about two years. But when they were kept with a mix of plants producing one toxin and plants producing two, the insects eventually developed resistance to both toxins.

According to Dr. Ahelton, single-gene plants really function as a steppingstone in resistance of twogene plants if the single-gene plants contain one of the same Bt proteins as the two-gene plant. Maize and cotton are the only commercial crops now engineered to contain the Bt proteins.

GM cassava uses viral gene to fight disease

A team of researchers led by Dr. Peng Zhang at the Swiss Federal Institute of Technology in Zurich, Switzerland, has used the viruss own genetic material as a weapon against it. They used genes from African cassava mosaic virus, which periodically devastates cassava crops in Africa to create cassava plants that could resist the virus. African cassava mosaic virus is transmitted to cassava by whiteflies when they feed on the plant. In parts of East and Central Africa, epidemics of the disease lead to total losses of harvests. The African cassava mosaic virus needs three genes to replicate. Each of these carries the code for a piece of RNA. RNA could be inactivated when a matching strand binds to it. Dr. Zhangs team created matching genes for the three crucial strands of RNA and inserted these into cassava plants. Whenever the modified cassava cells were infected by the virus, the RNA made by the inserted genes would find and stick to the viral RNA, inactivating it and preventing replication. In tests, when the plants were exposed to small amounts of the virus, the researchers could see no signs of disease, suggesting their theory was verified. Although the modified cassava plants were more resistant to the virus, experiments under natural conditions were needed to confirm the methods effectiveness.

Rice with human touch

Scientists at the National Institute of Agrobiological Sciences in Tsukumba, Tokyo, Japan, have incorporated a human gene into the rice genome to evolve a variety resistant to several herbicides.They took from the human liver the gene that codes for an enzyme called CPY2B6, which is particularly good at breaking down harmful chemicals in the body, and inserted it into the rice plant. They found that the gene gave the plant immunity to as many as 13 different herbicides. This would mean that weeds could be kept down by constantly changing the chemicals used, to prevent weeds building up resistance.

Down to Earth, 15 June 2005

PUBLICATIONS

Culture of Animal Cells: A Manual of Basic Technique

This 672 page fifth edition continues to offer most comprehensive information on the techniques, equipment, principles and practices of animal cell culture. It provides information related to growth of animal cells in tissue culture, beginning with laboratory design, safety and bioethics, and moving from preparation through to contamination, molecular techniques and troubleshooting. Both organ culture and cell culture are covered in this manual. A wide range of essential information from basic to specialized procedures is presented, highlighting advantages and limitations, and illustrating the properties of different types of culture.

Database Annotation in Molecular Biology: Principles and Practice

Two factors dominate current molecular biology: the amount of raw data is increasing very rapidly and applications in biomedical research require carefully curated and annotated databases. With the recognition of the importance of accurate database annotation and the requirement for individuals with particular constellations of skills to carry it out, annotators are emerging as specialists within the profession of bioinformatics.

This book compiles information about annotation its current status, what is required to improve it, what skills must be brought to bear on database curation and hence what is the proper training for annotators. The book should be essential reading for all people working on biological databases, both biologists and computer scientists. It will also be of use to all users of such databases, including molecular biologists, geneticists, protein chemists, clinicians and drug developers.